Added build instructions for more PRACE machines, corrected a link that has...

Added build instructions for more PRACE machines, corrected a link that has changed since the last review.

gpaw/build/examples/BSC-MareNostrum4-skylake/build_20.1.0_Python38_FFTW_icc.BSC.sh

+#!/bin/bash
+#
+# Installation script for GPAW 20.1.0:
+# * We compile our own Python as this is the best guarantee to not have to
+#   struggle with compatibility problems between various compilers used for
+#   various components
+# * Using the matching version of ase, 3.19.3
+# * Compiling with the Intel compilers
+#
+# The FFT library is discovered at runtime. With the settings used in this script
+# this should be MKL FFT, but it is possible to change this at runtime to either
+# MKL, FFTW or the built-in NumPy FFT routines, see the installation instructions
+# (link below).
+#
+# The original installation instructions for GPAW can be found at
+# https://gitlab.com/gpaw/gpaw/-/blob/20.1.0/doc/install.rst
+#
+
+packageID='20.1.0-Python38-FFTW-icc'
+packageName='GPAW-UEABS'
+
+echo -e "\n###### Building $packageName/$packageID from $0\n\n"
+
+# The next three variables are only used to load the right UEABS module
+# and to give example values for variable settings in comments.
+install_root=$PROJECT/UEABS
+systemID=BSC-MareNostrum4-skylake
+
+module purge
+MODULEPATH=$install_root/$systemID/Modules:$MODULEPATH
+
+#
+# The following UEABS_ variables are needed:
+# We set them manually as we have no UEABS module for this system at the moment.
+#
+# Directory to put the downloaded sources of the packages.
+UEABS_DOWNLOADS=$install_root/SOURCES
+# Directory where packages should be installed.
+UEABS_PACKAGES=$install_root/$systemID/Packages
+# Directory where modules are installed
+UEABS_MODULES=$install_root/$systemID/Modules
+
+install_dir=$UEABS_PACKAGES/$packageName/$packageID
+modules_dir=$UEABS_MODULES/$packageName
+#build_dir="/dev/shm/$USER/$packageName/$packageID"
+build_dir="$SCRATCH/UEABS-tmp/$packageName/$packageID"
+
+# Software versions
+python_version='3.8.7'
+zlib_version='1.2.11'
+ncurses_version='6.2'
+readline_version='8.0'
+sqlite_version='3.33.0'
+sqlite_download='3330000'
+libffi_version='3.3'
+fftw_version='3.3.8'
+libxc_version='4.3.4'
+
+setuptools_version='56.0.0'
+setuptoolsscm_version='6.0.1'
+wheel_version='0.35.1'
+
+attrs_version='20.3.0'
+pybind11_version='2.6.2'
+cython_version='0.29.21'
+
+py_version='1.10.0'
+pyparsing_version='2.4.7'
+toml_version='0.10.2'
+iniconfig_version='1.1.1'
+packaging_version='20.9'
+pytest_version='6.2.3'
+
+numpy_version='1.18.5'
+scipy_version='1.5.4'
+ase_version='3.19.3'
+GPAW_version='20.1.0'
+
+GPAWsetups_version='0.9.20000' # Check version on https://wiki.fysik.dtu.dk/gpaw/setups/setups.html
+
+# Compiler settings
+#compiler_module='intel/2020.1'
+#mpi_module='impi/2018.4'
+#math_module='mkl/2020.1'
+compiler_module='intel/2018.4'
+mpi_module='impi/2018.4'
+math_module='mkl/2018.4'
+opt_level='-O2'
+proc_opt_flags='-xHost'
+fp_opt_flags='-ftz -fp-speculation=safe -fp-model source'
+parallel=16
+
+py_maj_min='3.8'
+
+################################################################################
+#
+# Prepare the system
+#
+
+#
+# Load modules
+#
+mkdir -p $modules_dir
+module load $compiler_module
+module load $mpi_module
+module load $math_module
+
+#
+# Create the directories and make sure they are clean if that matters
+#
+/usr/bin/mkdir -p $UEABS_DOWNLOADS
+
+/usr/bin/mkdir -p $install_dir
+/usr/bin/rm -rf   $install_dir
+/usr/bin/mkdir -p $install_dir
+
+/usr/bin/mkdir -p $modules_dir
+
+/usr/bin/mkdir -p $build_dir
+/usr/bin/rm -rf   $build_dir
+/usr/bin/mkdir -p $build_dir
+
+
+################################################################################
+#
+# Download components
+#
+
+echo -e "\n### Downloading files...\n"
+
+function wget() {
+
+    echo "Please download $1 to $UEABS_DOWNLOADS"
+
+}
+
+cd $UEABS_DOWNLOADS
+
+downloads_OK=1
+
+# zlib: https://www.zlib.net/zlib-1.2.11.tar.gz
+zlib_file="zlib-$zlib_version.tar.gz"
+zlib_url="https://www.zlib.net"
+[[ -f $zlib_file ]] || wget "$zlib_url/$zlib_file"
+[[ -f $zlib_file ]] || downloads_OK=0
+
+# ncurses: https://ftp.gnu.org/pub/gnu/ncurses/ncurses-6.2.tar.gz
+ncurses_file="ncurses-$ncurses_version.tar.gz"
+ncurses_url="https://ftp.gnu.org/pub/gnu/ncurses"
+[[ -f $ncurses_file ]] || wget "$ncurses_url/$ncurses_file"
+[[ -f $ncurses_file ]] || downloads_OK=0
+
+# readline: https://ftp.gnu.org/pub/gnu/readline/readline-8.0.tar.gz
+readline_file="readline-$readline_version.tar.gz"
+readline_url="https://ftp.gnu.org/pub/gnu/readline"
+[[ -f $readline_file ]] || wget "$readline_url/$readline_file"
+[[ -f $readline_file ]] || downloads_OK=0
+
+# sqlite: https://www.sqlite.org/2020/sqlite-autoconf-3330000.tar.gz
+sqlite_file="sqlite-autoconf-$sqlite_download.tar.gz"
+sqlite_url="https://www.sqlite.org/2020"
+[[ -f $sqlite_file ]] || wget "$sqlite_url/$sqlite_file"
+[[ -f $sqlite_file ]] || downloads_OK=0
+
+# libffi: https://github.com/libffi/libffi/releases/download/v3.3/libffi-3.3.tar.gz
+libffi_file="libffi-$libffi_version.tar.gz"
+libffi_url="https://github.com/libffi/libffi/releases/download/v$libffi_version"
+[[ -f $libffi_file ]] || wget "$libffi_url/$libffi_file"
+[[ -f $libffi_file ]] || downloads_OK=0
+
+# FFTW: http://www.fftw.org/fftw-3.3.8.tar.gz
+fftw_file="fftw-$fftw_version.tar.gz"
+fftw_url="http://www.fftw.org"
+[[ -f $fftw_file ]] || wget "$fftw_url/$fftw_file"
+[[ -f $fftw_file ]] || downloads_OK=0
+
+# https://gitlab.com/libxc/libxc/-/archive/4.3.4/libxc-4.3.4.tar.bz2
+libxc_file="libxc-$libxc_version.tar.bz2"
+libxc_url="https://gitlab.com/libxc/libxc/-/archive/$libxc_version"
+[[ -f $libxc_file ]] || wget "$libxc_url/$libxc_file"
+[[ -f $libxc_file ]] || downloads_OK=0
+
+# Python: https://www.python.org/ftp/python/3.7.9/Python-3.7.9.tar.xz
+python_file="Python-$python_version.tar.xz"
+python_url="https://www.python.org/ftp/python/$python_version"
+[[ -f $python_file ]] || wget "$python_url/$python_file"
+[[ -f $python_file ]] || downloads_OK=0
+
+# Downloading setuptools.
+setuptools_file="setuptools-$setuptools_version.tar.gz"
+setuptools_url="https://pypi.python.org/packages/source/s/setuptools"
+[[ -f $setuptools_file ]] || wget $setuptools_url/$setuptools_file
+[[ -f $setuptools_file ]] || downloads_OK=0
+
+# Downloading setuptoolssscm so that we can gather all sources for reproducibility.
+setuptoolsscm_file="setuptools_scm-$setuptoolsscm_version.tar.gz"
+setuptoolsscm_url="https://pypi.python.org/packages/source/s/setuptools_scm"
+[[ -f $setuptoolsscm_file ]] || wget $setuptoolsscm_url/$setuptoolsscm_file
+[[ -f $setuptoolsscm_file ]] || downloads_OK=0
+
+# Downloading wheel so that we can gather all sources for reproducibility.
+wheel_file="wheel-$wheel_version.tar.gz"
+wheel_url="https://pypi.python.org/packages/source/w/wheel"
+[[ -f $wheel_file ]] || wget "$wheel_url/$wheel_file"
+[[ -f $wheel_file ]] || downloads_OK=0
+
+# Downloading attrs so that we can gather all sources for reproducibility.
+attrs_file="attrs-$attrs_version.tar.gz"
+attrs_url="https://pypi.python.org/packages/source/a/attrs"
+[[ -f $attrs_file ]] || wget $attrs_url/$attrs_file
+[[ -f $attrs_file ]] || downloads_OK=0
+
+# Downloading pybind11 so that we can gather all sources for reproducibility.
+pybind11_file="pybind11-$pybind11_version.tar.gz"
+pybind11_url="https://pypi.python.org/packages/source/p/pybind11"
+[[ -f $pybind11_file ]] || wget $pybind11_url/$pybind11_file
+[[ -f $pybind11_file ]] || downloads_OK=0
+
+# Downloading Cython so that we can gather all sources for reproducibility.
+cython_file="Cython-$cython_version.tar.gz"
+cython_url="https://pypi.python.org/packages/source/c/cython"
+[[ -f $cython_file ]] || wget "$cython_url/$cython_file"
+[[ -f $cython_file ]] || downloads_OK=0
+
+# Downloading py so that we can gather all sources for reproducibility.
+py_file="py-$py_version.tar.gz"
+py_url="https://pypi.python.org/packages/source/p/py"
+[[ -f $py_file ]] || wget $py_url/$py_file
+[[ -f $py_file ]] || downloads_OK=0
+
+# Downloading pyparsing so that we can gather all sources for reproducibility.
+pyparsing_file="pyparsing-$pyparsing_version.tar.gz"
+pyparsing_url="https://pypi.python.org/packages/source/p/pyparsing"
+[[ -f $pyparsing_file ]] || wget $pyparsing_url/$pyparsing_file
+[[ -f $pyparsing_file ]] || downloads_OK=0
+
+# Downloading toml so that we can gather all sources for reproducibility.
+toml_file="toml-$toml_version.tar.gz"
+toml_url="https://pypi.python.org/packages/source/t/toml"
+[[ -f $toml_file ]] || wget $toml_url/$toml_file
+[[ -f $toml_file ]] || downloads_OK=0
+
+# Downloading iniconfig so that we can gather all sources for reproducibility.
+iniconfig_file="iniconfig-$iniconfig_version.tar.gz"
+iniconfig_url="https://pypi.python.org/packages/source/i/iniconfig"
+[[ -f $iniconfig_file ]] || wget $iniconfig_url/$iniconfig_file
+[[ -f $iniconfig_file ]] || downloads_OK=0
+
+# Downloading packaging so that we can gather all sources for reproducibility.
+packaging_file="packaging-$packaging_version.tar.gz"
+packaging_url="https://pypi.python.org/packages/source/p/packaging"
+[[ -f $packaging_file ]] || wget $packaging_url/$packaging_file
+[[ -f $packaging_file ]] || downloads_OK=0
+
+# Downloading pytest so that we can gather all sources for reproducibility.
+pytest_file="pytest-$pytest_version.tar.gz"
+pytest_url="https://pypi.python.org/packages/source/p/pytest"
+[[ -f $pytest_file ]] || wget $pytest_url/$pytest_file
+[[ -f $pytest_file ]] || downloads_OK=0
+
+# NumPy needs customizations, so we need to download and unpack the sources
+numpy_file="numpy-$numpy_version.zip"
+numpy_url="https://pypi.python.org/packages/source/n/numpy"
+[[ -f $numpy_file ]] || wget "$numpy_url/$numpy_file"
+[[ -f $numpy_file ]] || downloads_OK=0
+
+# SciPy
+scipy_file="scipy-$scipy_version.tar.gz"
+scipy_url="https://pypi.python.org/packages/source/s/scipy"
+[[ -f $scipy_file ]] || wget "$scipy_url/$scipy_file"
+[[ -f $scipy_file ]] || downloads_OK=0
+
+# Downloading ase so that we can gather all sources for reproducibility
+ase_file="ase-$ase_version.tar.gz"
+ase_url="https://pypi.python.org/packages/source/a/ase"
+[[ -f $ase_file ]] || wget "$ase_url/$ase_file"
+[[ -f $ase_file ]] || downloads_OK=0
+
+# GPAW needs customization, so we need to download and unpack the sources.
+GPAW_file="gpaw-$GPAW_version.tar.gz"
+GPAW_url="https://pypi.python.org/packages/source/g/gpaw"
+[[ -f $GPAW_file ]] || wget "$GPAW_url/$GPAW_file"
+[[ -f $GPAW_file ]] || downloads_OK=0
+
+# Download GPAW-setup, a number of setup files for GPAW.
+# https://wiki.fysik.dtu.dk/gpaw-files/gpaw-setups-0.9.20000.tar.gz
+GPAWsetups_file="gpaw-setups-$GPAWsetups_version.tar.gz"
+GPAWsetups_url="https://wiki.fysik.dtu.dk/gpaw-files"
+[[ -f $GPAWsetups_file ]] || wget "$GPAWsetups_url/$GPAWsetups_file"
+[[ -f $GPAWsetups_file ]] || downloads_OK=0
+
+[[ $downloads_OK ]] || exit
+
+
+################################################################################
+#
+# Set PATH-style variables
+#
+/usr/bin/mkdir -p $install_dir/bin
+PATH="$install_dir/bin:$PATH"
+/usr/bin/mkdir -p $install_dir/lib
+LD_LIBRARY_PATH="$install_dir/lib:$LD_LIBRARY_PATH"
+export LIBRARY_PATH="$LD_LIBRARY_PATH"
+
+
+################################################################################
+#
+# Install ncurses
+#
+# We mirror the two-step EasyBuild install process. This may be overkill, but
+# we know it works.
+#
+
+echo -e "\n### Installing ncurses...\n"
+
+cd $build_dir
+
+# Uncompress
+tar -xf $UEABS_DOWNLOADS/$ncurses_file
+
+cd ncurses-$ncurses_version
+
+# Configure step 1
+export CC=icc
+export CFLAGS="$opt_level $proc_opt_flags $fp_opt_flags -fPIC"
+export CXX=icpc
+export CXXFLAGS="$opt_level $proc_opt_flags $fp_opt_flags -fPIC"
+./configure --prefix="$install_dir" \
+            --with-shared --enable-overwrite --without-ada --enable-symlinks
+
+# Build step 1
+make -j $parallel
+
+# Install step 1
+make install
+
+# Add bin, lib and include to the PATH variables
+PATH=$install_dir/bin:$PATH
+LIBRARY_PATH=$install_dir/lib:$LIBRARY_PATH
+LD_LIBRARY_PATH=$install_dir/lib:$LD_LIBRARY_PATH
+CPATH=$install_dir/include:$CPATH
+
+# Configure step 2
+make distclean
+./configure --prefix="$install_dir" \
+            --with-shared --enable-overwrite --without-ada --enable-symlinks \
+            --enable-ext-colors --enable-widec \
+            --includedir=$install_dir/include/ncursesw/
+
+# Build step 2
+make -j $parallel
+
+# Install step 2
+make install
+
+# Clean-up
+unset CC
+unset CFLAGS
+unset CXX
+unset CXXFLAGS
+echo -e "\n### Finishing ncurses installation...\n"
+
+
+################################################################################
+#
+# Install readline
+#
+
+echo -e "\n### Installing readline...\n"
+
+cd $build_dir
+
+# Uncompress
+tar -xf $UEABS_DOWNLOADS/$readline_file
+
+cd readline-$readline_version
+
+# Configure
+export CC=icc
+export CFLAGS="$opt_level $proc_opt_flags $fp_opt_flags -fPIC"
+export CPPFLAGS="-I$install_dir/include"
+export LDFLAGS="-L$install_dir/lib -lncurses"
+./configure --prefix="$install_dir"
+
+# Build
+make -j $parallel
+
+# Install
+make install
+
+# Clean-up
+unset CC
+unset CFLAGS
+unset CPPFLAGS
+unset LDFLAGS
+echo -e "\n### Finishing readline installation...\n"
+
+
+################################################################################
+#
+# Install zlib
+#
+
+echo -e "\n### Installing zlib...\n"
+
+cd $build_dir
+
+# Uncompress
+tar -xf $UEABS_DOWNLOADS/$zlib_file
+
+cd zlib-$zlib_version
+
+# Configure
+export CC=icc
+export CFLAGS="$opt_level $proc_opt_flags $fp_opt_flags -fPIC"
+./configure --prefix="$install_dir"
+
+# Build
+make -j $parallel
+
+# Install
+make install
+
+# Clean-up
+unset CC
+unset CFLAGS
+echo -e "\n### Finishing zlib installation...\n"
+
+
+################################################################################
+#
+# Install libffi
+#
+
+echo -e "\n### Installing libffi...\n"
+
+cd $build_dir
+
+# Uncompress
+tar -xf $UEABS_DOWNLOADS/$libffi_file
+
+cd libffi-$libffi_version
+
+# Configure
+export CC=icc
+export CFLAGS="$opt_level $proc_opt_flags $fp_opt_flags -fPIC"
+./configure --prefix="$install_dir" \
+            --disable-multi-os-directory
+
+# Build
+make -j $parallel
+
+# Install
+make install
+
+# Clean-up
+unset CC
+unset CFLAGS
+echo -e "\n### Finishing libffi installation...\n"
+
+
+################################################################################
+#
+# Install SQLite
+#
+
+echo -e "\n### Installing SQLite...\n"
+
+cd $build_dir
+
+# Uncompress
+tar -xf $UEABS_DOWNLOADS/$sqlite_file
+
+cd sqlite-autoconf-$sqlite_download
+
+# Configure
+export CC=icc
+export CFLAGS="$opt_level $proc_opt_flags $fp_opt_flags -fPIC -DSQLITE_DISABLE_INTRINSIC"
+export CPPFLAGS="-I$install_dir/include"
+./configure --prefix="$install_dir"
+
+# Build
+make -j $parallel
+
+# Install
+make install
+
+# Clean-up
+unset CC
+unset CFLAGS
+unset CPPFLAGS
+echo -e "\n### Finishing SQLite installation...\n"
+
+
+################################################################################
+#
+# Install FFTW
+#
+
+echo -e "\n### Installing FFTW...\n"
+
+cd $build_dir
+
+# Uncompress
+tar -xf $UEABS_DOWNLOADS/$fftw_file
+
+# Patch the sources to compile with icc
+cat >fftw.patch <<EOF
+avoid using -no-gcc when compiling FFTW with Intel compilers,
+since that fails on CentOS 8
+see https://github.com/easybuilders/easybuild-easyconfigs/issues/10932
+and https://github.com/FFTW/fftw3/issues/184
+--- fftw-3.3.8/configure.orig
++++ fftw-3.3.8/configure
+@@ -14861,6 +14861,9 @@
+    intel) # Stop icc from defining __GNUC__, except on MacOS where this fails
+         case "\${host_os}" in
+             *darwin*) ;; # icc -no-gcc fails to compile some system headers
++            # using -no-gcc with recent Intel compilers fails on CentOS 8,
++            # and was only needed as a workaround for old Intel compilers anyway
++            *linux*) ;;
+             *)
+ 	        { \$as_echo "\$as_me:\${as_lineno-\$LINENO}: checking whether C compiler accepts -no-gcc" >&5
+ $as_echo_n "checking whether C compiler accepts -no-gcc... " >&6; }
+
+EOF
+
+cd fftw-$fftw_version
+patch -p1 <../fftw.patch
+
+# Configure
+export CC=icc
+export CFLAGS="$opt_level $proc_opt_flags $fp_opt_flags -fPIC"
+export MPICC=mpiicc
+export F77=ifort
+export F77FLAGS="$opt_level $proc_opt_flags $fp_opt_flags -fPIC"
+./configure --prefix="$install_dir" \
+            --disable-sse --disable-sse2 --disable-avx --enable-avx2 --disable-avx512 --disable-avx-128-fma --disable-kcvi \
+            --enable-fma \
+            --disable-openmp --disable-threads \
+            --enable-mpi \
+            -disable-static --enable-shared --disable-fortran
+
+# Build
+make -j $parallel
+
+# Install
+make install
+
+# Clean-up
+unset CC
+unset CFLAGS
+unset MPICC
+unset F77
+unset F77FLAGS
+echo -e "\n### Finishing FFTW installation...\n"
+
+
+################################################################################
+#
+# Install libxc
+#
+
+echo -e "\n### Installing libxc...\n"
+
+cd $build_dir
+
+# Uncompress
+tar -xf $UEABS_DOWNLOADS/$libxc_file
+
+cd libxc-$libxc_version
+
+# Configure
+autoreconf -i
+
+export CC=icc
+export CFLAGS="$opt_level $proc_opt_flags $fp_opt_flags -fPIC"
+./configure --prefix="$install_dir" \
+            --disable-static --enable-shared --disable-fortran
+# Build
+make -j $parallel
+
+# Install
+make -j install
+
+# Clean-up
+unset CC
+